Discovery Environment

The Discovery Environment is a web portal for life science research, giving access to the data store and compute of the iPlant cyber-infrastructure.

This project contains all of the public code used in the Discovery Environment. That includes internally developed libraries, tools, services, database schemas and migrations, build tool plugins, GWT/GXT UI, and Ansible scripts.

All of the code in this project was previously available as separate git repositories at various granularities, but we decided to consolidate everything to make it easier to navigate, package, and manage. You can find the old repositories under the iPlantArchive organization, should you need them.

The top-level directories lein-plugins, libs, services, tools, databases, ui, and ansible are the categories that the code falls into. Each direct subdirectory contains a separate project. For instance, services/terrain/ contains the service that the Discovery Environment UI interacts with directly. Clojure project subfolders are Leiningen subprojects in and of themselves, and the UI subdirectory is a Gradle project.

Many subdirectories have their own README.md files which can be consulted if more specific information is desired.

UI

The Discovery Environment UI is the front-end GWT/GXT code with which a user directly interacts. This code lives under the ui subdirectory, and this section assumes that subdirectory is your present working directory.

This project is built with Gradle. Please refer to the Gradle documentation for an intro to the build script basics. The top level is itself a gradle project, but there are multiple sub-projects defined within.

In addition to the basic gradle build files, here is an explanation of our additions:

• versions.gradle: This contains common library version definitions for libraries used throughout the subprojects.
• iplant/webapps.gradle: Contains the sub-project definitions for the DE webapps.
• iplant/modules.gradle: Contains the sub-project definitions for the non-webapp projects used by the webapps.
• iplant/code-style: Contains code style definitions for the eclipse and idea environments.

Gradle basics

To find the list of tasks you can execute:

./gradlew tasks

Building everything

The webapp requires that the de.properties file be located in /etc/iplantc/de/.

To build and run the DE draft or prod self-executing war:

./gradlew runDraftWar
./gradlew runWar

To generate production war file:

./gradlew createProdWar # Resulting war will be in target/

To generate a GWT draft war file:

./gradlew draftBootRepackage

GWT Super Dev Mode

To start the Super Dev Mode code-server:

./gradlew :de:sdm

Once this code-server is started, you can use it to debug any of our wars which have source-maps enabled. Only the draft wars have source-maps enabled. For instructions on how to use Super Dev Mode, please refer to the GWT project site.

Backend

Development environment setup

You will need the following tools and plugins to develop for the DE backend.

• JDK 7: The backend code should work fine on either Oracle's JDK or on the OpenJDK.
• Leiningen: Clojure multi-tool. See http://leiningen.org/.
• Maven 3: Unfortunately not all of the backend code is in Clojure.
• lein-exec: A plugin for running stand-alone Clojure scripts. See https://github.com/kumarshantanu/lein-exec.
• lein-midje: A Clojure test framework. See https://github.com/marick/Midje.

For kifshare development, you will also need the following tools:

• node.js: A javascript runtime environment.
• npm: The node.js package manager
• grunt: A build tool for javascript projects.

The easiest way to get the above on OS X is with homebrew:

brew install npm
npm install -g grunt-cli
npm install -g grunt

If you intend to build the services with the build-all.clj script, you will need those tools installed.

Building everything

We've provided a Clojure script that will go through all of the projects, build them, and move the builds to a builds/ directory. You run it like this from the top level of this project:

lein exec build-all.clj

If you just want to create the Leiningen-compatible checkout symlinks, run the following command:

lein exec build-all.clj symlinks

To build just the services, run:

lein exec build-all.clj services

The rest:

lein exec build-all.clj tools
lein exec build-all.clj lein-plugins
lein exec build-all.clj libs
lein exec build-all.clj databases

To archive the builds into the builds/ directory, add the --archive option to the above commands.

lein exec build-all.clj tools --archive

Building a specific project

For the Leiningen projects, you'll want to create the checkouts symlinks first. They help make sure that you're developing against the latest version of our libraries.

lein exec build-all.clj symlinks

If you want to just build a specific project, go into the project's directory and call the appropriate build tool. For example:

cd services/terrain
lein clean
lein uberjar

(For libraries, you probably want lein install rather than uberjar.)

Setting and getting a version for everything

We've hacked together a bash script that will iterate over all of the Clojure projects and will set their versions to the same version, including the versions of the iPlant developed dependencies (aside from the apps service).

./set-version 2.0.10

Please, run that against a branch and submit a pull request.

We've also hacked a script together to report the versions of Clojure projects.

./get-versions

Again, these were hacked together extremely quickly and still have sharp edges. Be careful and do all modifications in a branch.

Ansible

These scripts are used to deploy all the other pieces of the Discovery Environment. Please consult the in-folder documentation for more details.